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Amino acids/Proteins

Amino acids/Proteins. Four Critical Biological Molecules. Sugars --------> polysaccharides Nucleotides --------> nucleic acids Fatty Acids --------> Lipids Amino acids -------> proteins. Amino Acids . Carboxyl. a. Amino. Sterioisomers.

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Amino acids/Proteins

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  1. Amino acids/Proteins

  2. Four Critical Biological Molecules Sugars --------> polysaccharides Nucleotides --------> nucleic acids Fatty Acids --------> Lipids Amino acids -------> proteins

  3. Amino Acids Carboxyl a Amino

  4. Sterioisomers The L amino acids have the amino grps to the left All three carbon atoms are in a row

  5. Non polar

  6. Aromatic

  7. Polar uncharged

  8. Polar positive a b g d e

  9. Polar negative

  10. Disulfide bonds

  11. Uncommon amino acids

  12. Zwitterions

  13. pI Each amino acid has a characteristic isoelectric point which is the pH at which the positive equals the negative charge. This varies based on the side chain. For amino acid without ionizable side chains (non-polar), the Isoelectric Point (equivalence point, pI) is pI= pK1+pK2/2 At this point, the net charge is zero. The AA is least soluble in water and the AA does not migrate in electric field (important in electrophoretic separation of peptides)

  14. Ionization and pH At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form. The R groups also gets protonated. This varies from amino acid to amino acid. Thus different amino acids have different pKa.

  15. Amino acid titration Amino acids with uncharged side-chains, such as glycine, have two pKa values: The pKa of the a-carboxyl group is 2.34 The pKa of the a-amino group is 9.6 It can act as a buffer in two pH regimes.

  16. R groups

  17. The pKa of the R group is designated here as pKR.

  18. Peptide bond formation Nucleophile= an atom or molecule that is electron-rich and seek positive charge

  19. Peptide bond resonance

  20. Peptide

  21. Peptides are 2-50 aa long Many peptides have function- hormones, neurotransmitters, sweetner Proteins are larger. Amino acids bind prosthetic groups such as metals, heme, phosphates etc.

  22. Conjugated Proteins

  23. Chromatography To understand a proteins, you need pure protein you need its sequence, you need its structure you need an assay to investigate activity.

  24. Ion exchange

  25. Gel Filtration (Size exclusion)

  26. Affinity

  27. SDS Gel Electrophoresis

  28. Isoelectric focusing

  29. Purification table

  30. Activity versus specific activity

  31. Structure

  32. Sequence

  33. Protein Consensus sequence

  34. Aligning sequences

  35. Peptide sequencing

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